[gmx-users] Problems with umbrella sampling
amarcovitz at gmail.com
Tue Dec 29 12:56:22 CET 2009
it seems to help, i have another general question that you might help me
should i define the distances for the umbrella sampling run in some file and
then run it?(i saw something about *.ppa file but couldn't find any further
instructions in the mannual..)
will this file apply for the WHAM analysis after the run?
On Mon, Dec 28, 2009 at 6:14 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Amir Marcovitz wrote:
>> my system is constructed of 2 parallel plates in a box with solvent. each
>> plate is made of 36 atoms which are positively charged on one of them (SRP)
>> and negatively charged on the other plate (SRN).
>> i want to perform a simulation with umbrella sampling between the 2 so i
>> defined the pulling section parameters in the .mdp parameter file as
>> ; COM PULLING ; Pull type: no, umbrella, constraint or
>> pull = umbrella
>> ; Pull geometry: distance, direction, cylinder or position
>> pull_geometry = distance
>> ; Select components for the pull vector. default: Y Y Y
>> pull_dim = Y Y Y
>> ; Cylinder radius for dynamic reaction force groups (nm)
>> pull_r1 = 1
>> ; Switch from r1 to r0 in case of dynamic reaction force
>> pull_r0 = 1.5
>> pull_constr_tol = 1e-06
>> pull_start = no
>> pull_nstxout = 10
>> pull_nstfout = 1
>> ; Number of pull groups
>> pull_ngroups = 2
>> ; Group name, weight (default all 1), vector, init, rate (nm/ps),
>> pull_group0 = SRP
>> pull_weights0 = 1
>> pull_pbcatom0 = 0
>> pull_group1 = SRN
>> pull_weights1 = 1
>> pull_pbcatom1 = 0
>> pull_vec1 = 0.0 1.0 0.0
>> pull_init1 = 1.5
>> pull_rate1 = 0
>> pull_k1 = 1
>> pull_kB1 = 0
>> when proccesing the file with grompp i get the following error:
>> *Fatal error:
>> Number of weights (1) for pull group 0 'SRP' does not match the number of
>> atoms (36)*
>> is someone recognizing my mistake?
> Please refer to the manual (manual.gromacs.org is quite handy), you will
> "Optional relative weights which are multiplied with the masses of the
> atoms to give the total weight for the COM. The number should be 0, meaning
> all 1, or the number of atoms in the pull group."
> I also think your value for pull_ngroup is wrong. It appears you are
> pulling SRN with respect to SRP, so you only have one pull group, not two.
> does someone has an experience with umbrella sampling in GROMACS?
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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